Marine protected management has gained acceptance as a way forward to achieve enhanced biodiversity outcomes. Simultaneously, co-management has gathered momentum as a mechanism to incorporate indigenous cultural aspirations within environmental management domains. Each management process has its own methodologies; when the two models intersect, they present a number of challenges to overall management outcomes. The authros review the journey of an indigenous co- management initiative within a marine protected area (MPA), the Great Barrier Reef World Heritage Area (GBRWHA), Australia, to explore how different management paradigms intersect with both negative and positive results. They argue that lessons learned from this initiative will help participants to adapt and innovate, so as to implement effective on ground management despite the region being a contested site.